Last updated: 2020-11-09

Checks: 7 0

Knit directory: T47D_ZR75_DHT_StrippedSerum_RNASeq/analysis/

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File Version Author Date Message
Rmd 9d03800 Steve Ped 2020-11-09 Added tabsets for both runs
Rmd 6f7af53 Steve Pederson 2020-11-06 Initial Commit

library(ngsReports)
library(tidyverse)
library(yaml)
library(scales)
library(pander)
library(glue)
library(plotly)
panderOptions("table.split.table", Inf)
panderOptions("big.mark", ",")
theme_set(theme_bw())
config <- here::here("config/config.yml") %>%
  read_yaml()
suffix <- paste0(config$tags$tag, config$ext)
sp <- config$ref$species %>%
  str_replace("(^[a-z])[a-z]*_([a-z]+)", "\\1\\2") %>%
  str_to_title()
samples <- config$samples %>%
  here::here() %>%
  read_tsv() %>%
  mutate(
    R1 = paste0(sample, config$tags$r1, suffix),
    R2 = paste0(sample, config$tags$r2, suffix),
  ) %>%
  pivot_longer(
    cols = c("R1", "R2"),
    names_to = "Reads",
    values_to = "Filename"
  )
config$analysis <- config$analysis %>%
  lapply(intersect, y = colnames(samples)) %>%
  .[vapply(., length, integer(1)) > 0]
if (length(config$analysis)) {
  samples <- samples %>%
    unite(
      col = group, 
      any_of(as.character(unlist(config$analysis))), 
      sep = "_", remove = FALSE
    )
} else {
  samples$group <- samples$Filename
}
group_cols <- hcl.colors(
  n = length(unique(samples$group)), 
  palette = "Zissou 1"
  ) %>%
  setNames(unique(samples$group))
fh <- round(6 + nrow(samples) / 15, 0)

Quality Assessment on Raw Data

Hiseq_1

rawFqc <- here::here("data/raw/FastQC/Hiseq_1") %>%
  list.files(pattern = "fastqc.zip", full.names = TRUE, recursive = TRUE) %>%
  FastqcDataList() %>%
  .[fqName(.) %in% samples$Filename]
plotSummary(rawFqc)
*Overall summary of FastQC reports*

Overall summary of FastQC reports

Library Sizes

A total of 32 libraries were contained in this dataset, with read totals ranging between 5,699,001 and 22,618,628 reads.

Across all libraries, reads were 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101 bases.

plotReadTotals(rawFqc, pattern = suffix, usePlotly = TRUE)

Library Sizes for all supplied fastq files. Any samples run as multiple libraries are shown as the supplied multiple libraries and have not been merged.

Sequence Quality

plotBaseQuals(
  rawFqc,
  pattern = suffix, 
  usePlotly = TRUE,
  dendrogram = TRUE,
  cluster = TRUE
  )

Mean sequencing quality scores at each base position for each library

GC Content

plotGcContent(
  x = rawFqc, 
  pattern = suffix, 
  species = sp, 
  gcType = "Trans",
  usePlotly = TRUE,
  dendrogram = TRUE,
  cluster = TRUE
  )

GC content shown as the % above and below the theoretical GC content for the Hsapiens transcriptome.

ggplotly(
  getModule(rawFqc, "Per_sequence_GC_content") %>%
    group_by(Filename) %>%
    mutate(
      cumulative = cumsum(Count) / sum(Count)
    ) %>%
    ungroup() %>%
    left_join(samples) %>%
    bind_rows(
      getGC(gcTheoretical, sp, "Trans") %>%
        mutate_at(sp, cumsum) %>% 
        rename_all(
          str_replace_all, 
          pattern = sp, replacement = "cumulative",
        ) %>%
        mutate(
          Filename = "Theoretical GC",
          group = Filename
        )
    ) %>%
    mutate(
      group = as.factor(group),
      group = relevel(group, ref = "Theoretical GC"),
      cumulative = round(cumulative*100, 2)
    ) %>%
    ggplot(aes(GC_Content, cumulative, group = Filename)) +
    geom_line(aes(colour = group), size = 1/3) +
    scale_x_continuous(label = ngsReports:::.addPercent) +
    scale_y_continuous(label = ngsReports:::.addPercent) +
    scale_colour_manual(
      values = c("#000000", group_cols)
    ) +
    labs(
      x = "GC Content",
      y = "Cumulative Total",
      colour = "Group"
    )
)

GC content shown as a cumulative distribution for all libraries. Groups can be hidden by clicking on them in the legend.

Sequence Content

plotly::ggplotly(
  getModule(rawFqc, module = "Per_base_sequence_content") %>% 
    mutate(Base = fct_inorder(Base)) %>%
    group_by(Base) %>% 
    mutate(
      across(c("A", "C", "G", "T"), function(x){x - mean(x)}) 
    ) %>% 
    pivot_longer(
      cols = c("A", "C", "G", "T"), 
      names_to = "Nuc", 
      values_to = "resid"
    ) %>%
    left_join(samples) %>%
    ggplot(
      aes(Base, resid, group = Filename, colour = group)
    ) + 
    geom_line() +
    facet_wrap(~Nuc) + 
    scale_colour_manual(values = group_cols) +
    labs(
      x = "Read Position", y = "Residual", colour = "Group"
    )
)

Base and Position specific residuals for each sample. The mean base content at each position was calculated for each nucleotide, and the sample-specific residuals calculated.

AdapterContent

plotAdapterContent(
  x = rawFqc, 
  pattern = suffix, 
  usePlotly = TRUE,
  dendrogram = TRUE,
  cluster = TRUE
  )

Total Adapter Content for each sample shown by starting position in the read.

Overrepresented Sequences

os <- suppressMessages(getModule(rawFqc, "Over"))
os_fh <- 6 + nrow(os) / 20
if (nrow(os)){
  if (length(unique(os$Filename)) > 1){
    suppressMessages(
      plotOverrep(
        x = rawFqc,
        pattern = suffix, 
        usePlotly = TRUE,
        dendrogram = TRUE,
        cluster = TRUE
      )
    )
  }
}

Summary of over-represented sequences across all libraries

os %>%
  group_by(Sequence, Possible_Source) %>%
  summarise(
    `Found in` = n(),
    Total = sum(Count),
    `Largest Percent` = glue("{round(max(Percentage), 2)}%")
  ) %>%
  pander(
    caption = "*Summary of over-represented sequences within the raw data.*"
  )
Summary of over-represented sequences within the raw data.
Sequence Possible_Source Found in Total Largest Percent
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA No Hit 1 19,652 0.34%
ACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAA No Hit 8 133,908 0.17%
ACTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG No Hit 3 32,989 0.15%
AGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTAC No Hit 1 7,719 0.13%
AGGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTA No Hit 1 12,229 0.21%
AGGGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT No Hit 1 14,213 0.25%
AGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG No Hit 1 8,843 0.15%
ATAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGGGCA No Hit 2 22,020 0.15%
ATAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAAGTAGGC No Hit 1 6,477 0.11%
ATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAA No Hit 1 8,818 0.14%
ATAGAGGTGATGTTTTTGGTAAACAGGCGGGGTAAGATTTGCCGAGTTCC No Hit 1 6,168 0.1%
ATATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTG No Hit 2 32,228 0.24%
ATCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGATTTTTTAGGTA No Hit 1 8,194 0.13%
ATCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT No Hit 1 11,028 0.11%
ATGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT No Hit 2 14,480 0.12%
ATTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGC No Hit 1 7,451 0.12%
ATTGGTTATAATTTTTCATCTTTCCCTTGCGGTACTATATCTATTGCGCC No Hit 2 25,859 0.19%
CAAACCCACTCCACCCTACTACCAGACAACCTTAGCCAAACCATTTACCC No Hit 1 15,502 0.1%
CAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCC No Hit 6 99,368 0.14%
CAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTG No Hit 11 147,514 0.13%
CACCAGGTTGCCTAAGGAGGGGTGAACCGGCCCAGGTCGGAAACGGAGCA No Hit 13 249,151 0.19%
CACTATTTTGCTACATAGACGGGTGTGCTCTTTTAGCTGTTCTTAGGTAG No Hit 6 94,649 0.13%
CACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTTTT No Hit 8 147,927 0.19%
CAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAG No Hit 9 133,258 0.13%
CAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAG No Hit 12 280,879 0.21%
CATTCTCCTCCGCATAAGCCTGCGTCAGATTAAGACACTGAACTGACAAT No Hit 1 15,559 0.11%
CCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACC No Hit 5 67,457 0.11%
CCAACACAGGCATGCCCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTC No Hit 1 15,886 0.11%
CCAAGATAGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAA No Hit 9 143,664 0.19%
CCACTATTTTGCTACATAGACGGGTGTGCTCTTTTAGCTGTTCTTAGGTA No Hit 9 137,591 0.14%
CCAGCTATCACCAGGCTCGGTAGGTTTGTCGCCTCTACCTATAAATCTTC No Hit 1 12,710 0.1%
CCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCA No Hit 13 459,777 0.46%
CCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACC No Hit 1 6,661 0.12%
CCCAAACCCACTCCACCCTACTACCAGACAACCTTAGCCAAACCATTTAC No Hit 8 322,329 0.4%
CCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTAC No Hit 8 476,575 0.54%
CCCAAATAAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATA No Hit 2 37,273 0.12%
CCCAACACAGGCATGCCCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACT No Hit 7 113,224 0.14%
CCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTTT No Hit 2 32,648 0.12%
CCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAACTA No Hit 3 41,439 0.12%
CCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG No Hit 8 118,340 0.14%
CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT No Hit 16 318,686 0.21%
CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT No Hit 6 94,359 0.15%
CCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC No Hit 1 15,336 0.13%
CCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTA No Hit 3 45,229 0.14%
CCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTT No Hit 12 231,034 0.2%
CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT No Hit 16 610,532 0.47%
CCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATA No Hit 6 91,213 0.16%
CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATT No Hit 16 574,447 0.48%
CCCTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCAT No Hit 7 260,551 0.38%
CCCTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCAT No Hit 7 280,267 0.47%
CCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGGGCATGCCTGTGTT No Hit 1 16,721 0.1%
CCGCACTAAGTTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCA No Hit 1 11,822 0.12%
CCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGTCC No Hit 3 50,876 0.13%
CCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTAC No Hit 1 6,976 0.12%
CCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCG No Hit 11 173,595 0.14%
CCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAG No Hit 5 87,355 0.15%
CCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAG No Hit 7 105,020 0.13%
CCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTG No Hit 16 395,723 0.31%
CCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTT No Hit 13 237,958 0.17%
CCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTA No Hit 8 146,451 0.19%
CCTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCATT No Hit 4 68,277 0.15%
CCTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCATT No Hit 3 71,447 0.21%
CCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAA No Hit 1 6,831 0.12%
CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG No Hit 16 1,215,558 0.87%
CCTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAA No Hit 1 7,128 0.13%
CCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCCTTGCGGTAC No Hit 12 262,326 0.23%
CGACCATCCCCGATAGAGGAGGACCGGTCTTCGGTCAAGGGTATACGAGT No Hit 1 7,089 0.12%
CGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGT No Hit 10 161,846 0.13%
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCT No Hit 11 170,329 0.14%
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCT No Hit 5 62,530 0.11%
CGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAA No Hit 3 59,609 0.13%
CGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGT No Hit 14 240,765 0.18%
CGGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTA No Hit 16 342,882 0.35%
CGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCA No Hit 2 24,946 0.12%
CGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACTTC No Hit 7 100,385 0.12%
CGTTAAACATGTGTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCT No Hit 6 99,704 0.15%
CGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTTCGCTTTGACTGG No Hit 14 303,781 0.22%
CTAACAGTTAAATTTACAAGGGGATTTAGAGGGTTCTGTGGGCAAATTTA No Hit 4 67,664 0.14%
CTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAAGTAGGC No Hit 1 8,611 0.14%
CTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAG No Hit 16 296,583 0.21%
CTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGA No Hit 6 90,920 0.12%
CTAGAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGTCA No Hit 11 192,513 0.18%
CTAGAGGTGATGTTTTTGGTAAACAGGCGGGGTAAGATTTGCCGAGTTCC No Hit 4 61,385 0.16%
CTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA No Hit 1 12,887 0.11%
CTCAGACCGCGTTCTCTCCCTCTCACTCCCCAATACGGAGAGAAGAACGA No Hit 11 274,101 0.31%
CTCAGATCACGTAGGACTTTAATCGTTGAACAAACGAACCTTTAATAGCG No Hit 12 214,174 0.19%
CTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC No Hit 12 292,345 0.24%
CTCATTTGGATGTGTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTC No Hit 14 258,172 0.21%
CTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAG No Hit 8 178,021 0.21%
CTCCGAGGTCGCCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGG No Hit 16 330,108 0.25%
CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT No Hit 16 623,795 0.39%
CTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGA No Hit 16 621,595 0.55%
CTCGCTATGTTGCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATC No Hit 7 108,012 0.13%
CTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGT No Hit 5 53,697 0.11%
CTCGGAGGTTGGGTTCTGCTCCGAGGTCGCCCCAACCGAAATTTTTAATG No Hit 10 181,804 0.17%
CTCGTATACCCTTGACCGAAGACCGGTCCTCCTCTATCGGGGATGGTCGT No Hit 1 16,776 0.1%
CTCGTCTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTT No Hit 9 160,533 0.2%
CTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCT No Hit 13 252,600 0.23%
CTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGCTGTTCCTCTTTGGACTA No Hit 3 55,562 0.12%
CTCTAGAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGT No Hit 15 381,300 0.27%
CTCTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGCTGTTCCTCTTTGGAC No Hit 16 494,532 0.35%
CTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACT No Hit 16 385,293 0.27%
CTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACTTCAAATTC No Hit 10 152,647 0.14%
CTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGT No Hit 10 168,308 0.14%
CTGCTGTTTCCCGTGGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATT No Hit 8 160,451 0.23%
CTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCG No Hit 6 74,003 0.11%
CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT No Hit 16 763,135 0.64%
CTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGA No Hit 5 65,325 0.11%
CTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTTTTTG No Hit 4 61,267 0.16%
CTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCAT No Hit 15 352,683 0.23%
CTGGTGATGCTAGAGGTGATGTTTTTGGTAAACAGGCGGGGTAAGATTTG No Hit 1 5,776 0.1%
CTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGT No Hit 14 316,880 0.29%
CTGTGGGCAAATTTAAAGTTGAACTAAGATTCTATCTTGGACAACCAGCT No Hit 3 31,305 0.12%
CTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCATTT No Hit 4 100,727 0.24%
CTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCATTT No Hit 7 147,120 0.2%
CTTAATCTGACGCAGGCTTATGCGGAGGAGAATGTTTTCATGTTACTTAT No Hit 3 43,738 0.13%
CTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATGAC No Hit 6 94,100 0.13%
CTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAAC No Hit 9 169,128 0.18%
CTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCATTATGCA No Hit 4 62,197 0.19%
CTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGC No Hit 15 463,555 0.38%
CTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAA No Hit 2 39,372 0.14%
CTTATGAGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGT No Hit 4 75,653 0.16%
CTTATGGGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGT No Hit 2 30,622 0.12%
CTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAA No Hit 16 337,454 0.24%
CTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGAC No Hit 3 30,234 0.12%
CTTCTATAGGGTGATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTAT No Hit 4 54,865 0.11%
CTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCT No Hit 1 15,174 0.12%
CTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCC No Hit 15 328,946 0.21%
CTTGGTTATAATTTTTCATCTTTCCCTTGCGGTACTATATCTATTGCGCC No Hit 14 423,849 0.51%
CTTTAATCGTTGAACAAACGAACCTTTAATAGCGGCTGCACCATCGGGAT No Hit 15 293,109 0.21%
CTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAAC No Hit 6 87,749 0.12%
CTTTCCTTATGAGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGA No Hit 6 110,254 0.18%
CTTTCCTTATGGGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGA No Hit 7 172,641 0.23%
CTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAACCGACCTGGATTACT No Hit 12 231,215 0.21%
GAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTC No Hit 7 95,555 0.13%
GATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGATT No Hit 4 78,926 0.2%
GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT No Hit 1 14,949 0.1%
GCCTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGA No Hit 2 20,086 0.12%
GCTACCTTTGCACGGTTAGGGTACCGCGGCCGTTAAACATGTGTCACTGG No Hit 10 228,397 0.21%
GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG No Hit 1 16,405 0.11%
GCTGCTTTTAGGCCTACTATGGGTGTTAAATTTTTTACTCTCTCTACAAG No Hit 6 104,245 0.14%
GCTGTTAATTGTCAGTTCAGTGTCTTAATCTGACGCAGGCTTATGCGGAG No Hit 1 7,926 0.14%
GGCAAATTTAAAGTTGAACTAAGATTCTATCTTGGACAACCAGCTATCAC No Hit 5 90,918 0.16%
GGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACC No Hit 1 20,892 0.14%
GGCTGCACCATCGGGATGTCCTGATCCAACATCGAGGTCGTAAACCCTAT No Hit 1 13,281 0.11%
GGCTGCTTTTAGGCCTACTATGGGTGTTAAATTTTTTACTCTCTCTACAA No Hit 2 40,662 0.15%
GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA No Hit 3 71,259 0.19%
GGCTTATGCGGAGGAGAATGTTTTCATGTTACTTATACTAACATTAGTTC No Hit 1 21,986 0.1%
GGGAAGCTCATCAGTGGGGCCACGAGCTGAGTGCGTCCTGTCACTCCACT No Hit 1 16,984 0.12%
GGGATTTAGAGGGTTCTGTGGGCAAATTTAAAGTTGAACTAAGATTCTAT No Hit 1 21,473 0.1%
GGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTAC No Hit 5 87,847 0.13%
GGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCAT No Hit 2 44,121 0.15%
GGGGTTAGTCCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCC No Hit 1 23,334 0.11%
GGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG No Hit 6 180,914 0.32%
GGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG No Hit 4 103,636 0.23%
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA No Hit 10 158,914 0.13%
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA No Hit 2 28,505 0.11%
GGTTAGTCCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCCTT No Hit 2 36,265 0.1%
GGTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTCTTAATCT No Hit 1 6,386 0.11%
GTAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGAGCA No Hit 5 112,114 0.2%
GTAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGGGCA No Hit 7 179,554 0.28%
GTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTG No Hit 8 208,260 0.26%
GTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTG No Hit 1 14,949 0.1%
GTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTT No Hit 3 51,730 0.11%
GTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGATTTTTTAGGTA No Hit 10 205,131 0.28%
GTCCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCCTTGCGGT No Hit 1 11,330 0.1%
GTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAACCGACCTGGATT No Hit 7 150,702 0.17%
GTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACC No Hit 8 144,018 0.18%
GTCTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTA No Hit 1 6,480 0.11%
GTGAGGAGTTCAGTTATATGTTTGGGATTTTTTAGGTAGTGGGTGTTGAG No Hit 1 6,202 0.11%
GTGCTCTTTTAGCTGTTCTTAGGTAGCTCGTCTGGTTTCGGGGGTCTTAG No Hit 8 142,697 0.19%
GTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT No Hit 2 22,531 0.18%
GTGGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT No Hit 7 193,790 0.28%
GTGGGTGTTGAGCTTGAACGCTTTCTTAATTGGTGGCTGCTTTTAGGCCT No Hit 2 21,915 0.12%
GTTAAACATGTGTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTA No Hit 1 15,312 0.1%
GTTAAATTTTTTACTCTCTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGC No Hit 1 5,887 0.1%
GTTAATTGTCAGTTCAGTGTCTTAATCTGACGCAGGCTTATGCGGAGGAG No Hit 4 67,302 0.16%
GTTAATTGTCAGTTCAGTGTTTTAATCTGACGCAGGCTTATGCGGAGGAG No Hit 1 17,391 0.12%
GTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGG No Hit 15 308,472 0.2%
GTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTAGATATTGGGC No Hit 1 6,064 0.11%
GTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTCTTAATCTG No Hit 2 27,541 0.14%
GTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTTTTAATCTG No Hit 1 18,241 0.12%
TGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACT No Hit 1 18,589 0.12%
TGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAGACACTGAACT No Hit 8 123,241 0.15%
TGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGGAGGGGTGA No Hit 1 11,462 0.11%

Hiseq_2

rawFqc <- here::here("data/raw/FastQC/Hiseq_2") %>%
  list.files(pattern = "fastqc.zip", full.names = TRUE, recursive = TRUE) %>%
  FastqcDataList() %>%
  .[fqName(.) %in% samples$Filename]
plotSummary(rawFqc)
*Overall summary of FastQC reports*

Overall summary of FastQC reports

Library Sizes

A total of 32 libraries were contained in this dataset, with read totals ranging between 10,944,091 and 28,623,352 reads.

Across all libraries, reads were 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101 bases.

plotReadTotals(rawFqc, pattern = suffix, usePlotly = TRUE)

Library Sizes for all supplied fastq files. Any samples run as multiple libraries are shown as the supplied multiple libraries and have not been merged.

Sequence Quality

plotBaseQuals(
  rawFqc,
  pattern = suffix, 
  usePlotly = TRUE,
  dendrogram = TRUE,
  cluster = TRUE
  )

Mean sequencing quality scores at each base position for each library

GC Content

plotGcContent(
  x = rawFqc, 
  pattern = suffix, 
  species = sp, 
  gcType = "Trans",
  usePlotly = TRUE,
  dendrogram = TRUE,
  cluster = TRUE
  )

GC content shown as the % above and below the theoretical GC content for the Hsapiens transcriptome.

ggplotly(
  getModule(rawFqc, "Per_sequence_GC_content") %>%
    group_by(Filename) %>%
    mutate(
      cumulative = cumsum(Count) / sum(Count)
    ) %>%
    ungroup() %>%
    left_join(samples) %>%
    bind_rows(
      getGC(gcTheoretical, sp, "Trans") %>%
        mutate_at(sp, cumsum) %>% 
        rename_all(
          str_replace_all, 
          pattern = sp, replacement = "cumulative",
        ) %>%
        mutate(
          Filename = "Theoretical GC",
          group = Filename
        )
    ) %>%
    mutate(
      group = as.factor(group),
      group = relevel(group, ref = "Theoretical GC"),
      cumulative = round(cumulative*100, 2)
    ) %>%
    ggplot(aes(GC_Content, cumulative, group = Filename)) +
    geom_line(aes(colour = group), size = 1/3) +
    scale_x_continuous(label = ngsReports:::.addPercent) +
    scale_y_continuous(label = ngsReports:::.addPercent) +
    scale_colour_manual(
      values = c("#000000", group_cols)
    ) +
    labs(
      x = "GC Content",
      y = "Cumulative Total",
      colour = "Group"
    )
)

GC content shown as a cumulative distribution for all libraries. Groups can be hidden by clicking on them in the legend.

Sequence Content

plotly::ggplotly(
  getModule(rawFqc, module = "Per_base_sequence_content") %>% 
    mutate(Base = fct_inorder(Base)) %>%
    group_by(Base) %>% 
    mutate(
      across(c("A", "C", "G", "T"), function(x){x - mean(x)}) 
    ) %>% 
    pivot_longer(
      cols = c("A", "C", "G", "T"), 
      names_to = "Nuc", 
      values_to = "resid"
    ) %>%
    left_join(samples) %>%
    ggplot(
      aes(Base, resid, group = Filename, colour = group)
    ) + 
    geom_line() +
    facet_wrap(~Nuc) + 
    scale_colour_manual(values = group_cols) +
    labs(
      x = "Read Position", y = "Residual", colour = "Group"
    )
)

Base and Position specific residuals for each sample. The mean base content at each position was calculated for each nucleotide, and the sample-specific residuals calculated.

AdapterContent

plotAdapterContent(
  x = rawFqc, 
  pattern = suffix, 
  usePlotly = TRUE,
  dendrogram = TRUE,
  cluster = TRUE
  )

Total Adapter Content for each sample shown by starting position in the read.

Overrepresented Sequences

os <- suppressMessages(getModule(rawFqc, "Over"))
os_fh <- 6 + nrow(os) / 20
if (nrow(os)){
  if (length(unique(os$Filename)) > 1){
    suppressMessages(
      plotOverrep(
        x = rawFqc,
        pattern = suffix, 
        usePlotly = TRUE,
        dendrogram = TRUE,
        cluster = TRUE
      )
    )
  }
}

Summary of over-represented sequences across all libraries

os %>%
  group_by(Sequence, Possible_Source) %>%
  summarise(
    `Found in` = n(),
    Total = sum(Count),
    `Largest Percent` = glue("{round(max(Percentage), 2)}%")
  ) %>%
  pander(
    caption = "*Summary of over-represented sequences within the raw data.*"
  )
Summary of over-represented sequences within the raw data.
Sequence Possible_Source Found in Total Largest Percent
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA No Hit 1 93,244 0.42%
ACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAA No Hit 8 173,813 0.16%
ACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAAGTAGG No Hit 1 17,151 0.1%
ATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAA No Hit 1 30,784 0.18%
CAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCC No Hit 6 127,777 0.14%
CAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTG No Hit 14 260,671 0.14%
CACCAGGTTGCCTAAGGAGGGGTGAACCGGCCCAGGTCGGAAACGGAGCA No Hit 13 302,526 0.21%
CACTAAGTTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCACCA No Hit 2 27,331 0.11%
CACTATTTTGCTACATAGACGGGTGTGCTCTTTTAGCTGTTCTTAGGTAG No Hit 2 28,395 0.1%
CACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTTTT No Hit 8 169,158 0.15%
CAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAG No Hit 13 241,299 0.14%
CAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAG No Hit 13 418,818 0.27%
CATCAATATGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGG No Hit 1 15,507 0.11%
CATTCTCCTCCGCATAAGCCTGCGTCAGATTAAGACACTGAACTGACAAT No Hit 1 14,303 0.1%
CCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACC No Hit 4 71,126 0.11%
CCAACACAGGCATGCCCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTC No Hit 1 14,514 0.1%
CCAAGATAGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAA No Hit 7 158,572 0.2%
CCACTATTTTGCTACATAGACGGGTGTGCTCTTTTAGCTGTTCTTAGGTA No Hit 7 114,629 0.12%
CCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCA No Hit 13 582,257 0.53%
CCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACC No Hit 1 24,383 0.11%
CCCAAACCCACTCCACCCTACTACCAGACAACCTTAGCCAAACCATTTAC No Hit 8 407,385 0.39%
CCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTAC No Hit 8 606,167 0.56%
CCCAAATAAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATA No Hit 3 51,957 0.12%
CCCAACACAGGCATGCCCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACT No Hit 7 121,940 0.13%
CCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAACTA No Hit 1 11,845 0.11%
CCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG No Hit 9 169,932 0.14%
CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT No Hit 16 478,697 0.25%
CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT No Hit 8 191,307 0.18%
CCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC No Hit 1 12,552 0.1%
CCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTA No Hit 3 68,210 0.14%
CCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTT No Hit 13 252,438 0.16%
CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT No Hit 16 894,791 0.53%
CCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATA No Hit 7 129,744 0.16%
CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATT No Hit 16 807,766 0.5%
CCCTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCAT No Hit 8 380,667 0.4%
CCCTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCAT No Hit 8 378,849 0.36%
CCGCACTAAGTTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCA No Hit 1 17,136 0.14%
CCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGTCC No Hit 5 91,285 0.13%
CCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTAC No Hit 1 27,978 0.12%
CCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCG No Hit 13 260,012 0.15%
CCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAG No Hit 7 137,481 0.13%
CCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAG No Hit 5 85,427 0.12%
CCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTG No Hit 16 593,917 0.3%
CCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTT No Hit 16 366,918 0.19%
CCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG No Hit 1 23,698 0.11%
CCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTA No Hit 7 154,193 0.16%
CCTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCATT No Hit 6 124,052 0.16%
CCTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCATT No Hit 7 128,236 0.16%
CCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAA No Hit 1 26,038 0.12%
CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG No Hit 16 1,559,454 0.88%
CCTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAA No Hit 1 25,086 0.11%
CCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCCTTGCGGTAC No Hit 9 221,481 0.2%
CGACCATCCCCGATAGAGGAGGACCGGTCTTCGGTCAAGGGTATACGAGT No Hit 1 18,094 0.11%
CGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGT No Hit 12 246,347 0.14%
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCT No Hit 16 347,546 0.17%
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCT No Hit 6 117,309 0.14%
CGCTATGTTGCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCC No Hit 2 27,049 0.1%
CGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAA No Hit 4 74,579 0.12%
CGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGT No Hit 2 41,069 0.1%
CGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGT No Hit 15 349,005 0.21%
CGGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTA No Hit 16 457,904 0.37%
CGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCA No Hit 1 21,393 0.13%
CGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACTTC No Hit 6 111,524 0.13%
CGTTAAACATGTGTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCT No Hit 6 113,034 0.14%
CGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTTCGCTTTGACTGG No Hit 16 436,986 0.22%
CTAACAGTTAAATTTACAAGGGGATTTAGAGGGTTCTGTGGGCAAATTTA No Hit 1 13,568 0.11%
CTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAAGTAGGC No Hit 1 29,724 0.18%
CTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGC No Hit 2 28,325 0.1%
CTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAG No Hit 16 368,003 0.21%
CTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGA No Hit 4 63,221 0.11%
CTAGAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGTCA No Hit 7 128,374 0.14%
CTAGAGGTGATGTTTTTGGTAAACAGGCGGGGTAAGATTTGCCGAGTTCC No Hit 5 98,294 0.15%
CTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA No Hit 1 11,492 0.1%
CTCAGACCGCGTTCTCTCCCTCTCACTCCCCAATACGGAGAGAAGAACGA No Hit 12 315,306 0.3%
CTCAGATCACGTAGGACTTTAATCGTTGAACAAACGAACCTTTAATAGCG No Hit 10 183,605 0.17%
CTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC No Hit 13 427,555 0.27%
CTCATTTGGATGTGTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTC No Hit 15 352,489 0.24%
CTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAG No Hit 8 219,119 0.21%
CTCCGAGGTCGCCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGG No Hit 16 448,496 0.25%
CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT No Hit 16 1,043,647 0.53%
CTCCTCTATCGGGGATGGTCGTCCTCTTCGACCGAGCGCGCAGCTTCGGG No Hit 4 57,003 0.11%
CTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGA No Hit 16 929,900 0.63%
CTCGCTATGTTGCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATC No Hit 5 76,656 0.13%
CTCGCTATGTTGCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATC No Hit 12 225,576 0.15%
CTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGT No Hit 1 24,681 0.11%
CTCGGAGGTTGGGTTCTGCTCCGAGGTCGCCCCAACCGAAATTTTTAATG No Hit 11 204,684 0.19%
CTCGTCTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTT No Hit 9 184,963 0.19%
CTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCT No Hit 15 365,271 0.23%
CTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGCTGTTCCTCTTTGGACTA No Hit 1 12,457 0.1%
CTCTAGAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGT No Hit 16 447,090 0.25%
CTCTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGCTGTTCCTCTTTGGAC No Hit 16 553,925 0.3%
CTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACT No Hit 16 508,514 0.3%
CTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCT No Hit 1 12,628 0.11%
CTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACTTCAAATTC No Hit 10 200,257 0.15%
CTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGT No Hit 14 322,060 0.21%
CTGCTGTTTCCCGTGGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATT No Hit 13 319,794 0.24%
CTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCG No Hit 12 202,974 0.12%
CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT No Hit 16 1,106,317 0.63%
CTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACG No Hit 1 13,698 0.11%
CTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGA No Hit 11 211,638 0.14%
CTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTTTTTG No Hit 4 75,891 0.12%
CTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCAT No Hit 15 477,543 0.26%
CTGGTGATGCTAGAGGTGATGTTTTTGGTAAACAGGCGGGGTAAGATTTG No Hit 1 25,606 0.11%
CTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAACTTAGT No Hit 1 12,518 0.1%
CTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGT No Hit 16 460,212 0.29%
CTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGG No Hit 1 20,247 0.1%
CTGTGGGCAAATTTAAAGTTGAACTAAGATTCTATCTTGGACAACCAGCT No Hit 2 42,223 0.11%
CTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTAG No Hit 1 17,726 0.1%
CTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCATTT No Hit 7 177,657 0.27%
CTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCATTT No Hit 8 261,048 0.23%
CTTAATCTGACGCAGGCTTATGCGGAGGAGAATGTTTTCATGTTACTTAT No Hit 2 26,244 0.12%
CTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATGAC No Hit 8 140,910 0.14%
CTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAAC No Hit 8 189,049 0.18%
CTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCATTATGCA No Hit 5 107,292 0.2%
CTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGC No Hit 15 709,970 0.47%
CTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAA No Hit 4 72,194 0.13%
CTTATGAGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGT No Hit 7 135,664 0.15%
CTTATGGGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGT No Hit 4 63,705 0.12%
CTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAA No Hit 16 587,783 0.35%
CTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGAC No Hit 1 28,315 0.13%
CTTCTATAGGGTGATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTAT No Hit 3 41,379 0.12%
CTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCT No Hit 4 71,784 0.13%
CTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCC No Hit 15 439,915 0.23%
CTTGGTTATAATTTTTCATCTTTCCCTTGCGGTACTATATCTATTGCGCC No Hit 16 651,782 0.5%
CTTTAATCGTTGAACAAACGAACCTTTAATAGCGGCTGCACCATCGGGAT No Hit 16 398,140 0.21%
CTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAAC No Hit 6 107,720 0.12%
CTTTCCTTATGAGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGA No Hit 7 158,822 0.17%
CTTTCCTTATGGGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGA No Hit 8 247,743 0.25%
CTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAACCGACCTGGATTACT No Hit 14 312,084 0.22%
CTTTGCACGGTTAGGGTACCGCGGCCGTTAAACATGTGTCACTGGGCAGG No Hit 2 25,395 0.11%
GAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTC No Hit 6 111,062 0.12%
GATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGATT No Hit 10 207,758 0.21%
GCACGGTTAGGGTACCGCGGCCGTTAAACATGTGTCACTGGGCAGGCGGT No Hit 1 12,994 0.11%
GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT No Hit 1 16,483 0.11%
GCCTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGA No Hit 2 47,035 0.16%
GCTACCTTTGCACGGTTAGGGTACCGCGGCCGTTAAACATGTGTCACTGG No Hit 13 335,892 0.21%
GCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCT No Hit 1 17,739 0.12%
GCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT No Hit 1 17,185 0.12%
GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG No Hit 4 60,763 0.15%
GCTGCTTTTAGGCCTACTATGGGTGTTAAATTTTTTACTCTCTCTACAAG No Hit 6 109,346 0.14%
GCTGTTAATTGTCAGTTCAGTGTCTTAATCTGACGCAGGCTTATGCGGAG No Hit 1 32,093 0.14%
GGATTTTTTAGGTAGTGGGTGTTGAGCTTGAACGCTTTCTTAATTGGTGG No Hit 1 23,649 0.12%
GGCAAATTTAAAGTTGAACTAAGATTCTATCTTGGACAACCAGCTATCAC No Hit 7 159,774 0.17%
GGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACC No Hit 1 21,198 0.15%
GGCTGCACCATCGGGATGTCCTGATCCAACATCGAGGTCGTAAACCCTAT No Hit 1 12,431 0.11%
GGCTGCTTTTAGGCCTACTATGGGTGTTAAATTTTTTACTCTCTCTACAA No Hit 1 12,914 0.12%
GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA No Hit 3 67,584 0.19%
GGGAAGCTCATCAGTGGGGCCACGAGCTGAGTGCGTCCTGTCACTCCACT No Hit 1 17,749 0.12%
GGGATTTAGAGGGTTCTGTGGGCAAATTTAAAGTTGAACTAAGATTCTAT No Hit 2 35,530 0.1%
GGGATTTTTTAGGTAGTGGGTGTTGAGCTTGAACGCTTTCTTAATTGGTG No Hit 1 26,849 0.12%
GGGGATTTAGAGGGTTCTGTGGGCAAATTTAAAGTTGAACTAAGATTCTA No Hit 1 22,819 0.1%
GGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTAC No Hit 4 75,442 0.13%
GGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCAT No Hit 3 62,401 0.14%
GGGGTTAGTCCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCC No Hit 1 20,509 0.1%
GGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG No Hit 8 294,859 0.3%
GGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG No Hit 6 158,012 0.21%
GGGTGATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGG No Hit 1 22,640 0.1%
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA No Hit 13 288,399 0.18%
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA No Hit 6 95,992 0.14%
GGTTAGTCCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCCTT No Hit 2 36,291 0.11%
GGTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTCTTAATCT No Hit 1 28,119 0.13%
GTAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGAGCA No Hit 8 215,866 0.22%
GTAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGGGCA No Hit 8 321,673 0.33%
GTAATAATGACTTGTTGGTTGATTGTAGATATTGGGCTGTTAATTGTCAG No Hit 2 32,467 0.12%
GTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTG No Hit 8 392,248 0.44%
GTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTG No Hit 2 32,126 0.12%
GTCAAGTTATTGGATCAATTGAGTATAGTAGTTCGCTTTGACTGGTGAAG No Hit 9 161,582 0.13%
GTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTT No Hit 5 85,663 0.12%
GTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGATTTTTTAGGTA No Hit 15 414,966 0.29%
GTCCGCACTAAGTTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGAC No Hit 1 15,267 0.11%
GTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAACCGACCTGGATT No Hit 13 281,258 0.18%
GTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACC No Hit 15 312,082 0.2%
GTCTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTA No Hit 5 92,344 0.13%
GTCTGTTCCAAGCTCCGGCAAAGGAGGCATCCGCCGGGCCCCTCCCCGAA No Hit 1 16,802 0.12%
GTGAGGAGTTCAGTTATATGTTTGGGATTTTTTAGGTAGTGGGTGTTGAG No Hit 1 27,307 0.12%
GTGATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGA No Hit 1 22,867 0.1%
GTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCATCAATATGGTG No Hit 2 28,998 0.12%
GTGCTCTTTTAGCTGTTCTTAGGTAGCTCGTCTGGTTTCGGGGGTCTTAG No Hit 13 317,419 0.21%
GTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGAT No Hit 4 66,105 0.12%
GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA No Hit 7 133,657 0.18%
GTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT No Hit 7 171,068 0.25%
GTGGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT No Hit 8 354,207 0.37%
GTGGGTGTTGAGCTTGAACGCTTTCTTAATTGGTGGCTGCTTTTAGGCCT No Hit 8 165,631 0.15%
GTTAAACATGTGTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTA No Hit 2 29,070 0.11%
GTTAAATTTTTTACTCTCTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGC No Hit 3 61,549 0.14%
GTTAATTGTCAGTTCAGTGTCTTAATCTGACGCAGGCTTATGCGGAGGAG No Hit 7 172,454 0.23%
GTTAATTGTCAGTTCAGTGTTTTAATCTGACGCAGGCTTATGCGGAGGAG No Hit 1 18,826 0.14%
GTTCCTTTTACTTTTTTTAACCTTTCCTTATGGGCATGCCTGTGTTGGGT No Hit 1 23,023 0.1%
GTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGG No Hit 15 417,024 0.23%
GTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTAGATATTGGGC No Hit 3 57,903 0.14%
GTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTCTTAATCTG No Hit 7 167,214 0.17%
GTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTTTTAATCTG No Hit 2 39,283 0.15%
GTTGGGTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTAGATAT No Hit 2 41,367 0.11%
GTTTTTGGTAAACAGGCGGGGTAAGATTTGCCGAGTTCCTTTTACTTTTT No Hit 2 35,451 0.12%
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN No Hit 10 460,429 0.43%
TATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGA No Hit 3 56,996 0.13%
TCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCA No Hit 1 14,689 0.12%
TCCAGGTCGGTTTCTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAA No Hit 1 13,043 0.11%
TGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACT No Hit 1 16,358 0.12%
TGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAGACACTGAACT No Hit 8 159,789 0.15%
TGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGAC No Hit 1 12,122 0.1%
TGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGGAGGGGTGA No Hit 1 16,601 0.14%
TGTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCT No Hit 1 25,034 0.11%
TTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTT No Hit 1 22,823 0.1%

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] plotly_4.9.2.1      glue_1.4.2          pander_0.6.3       
 [4] scales_1.1.1        yaml_2.2.1          forcats_0.5.0      
 [7] stringr_1.4.0       dplyr_1.0.2         purrr_0.3.4        
[10] readr_1.4.0         tidyr_1.1.2         tidyverse_1.3.0    
[13] ngsReports_1.6.0    tibble_3.0.4        ggplot2_3.3.2      
[16] BiocGenerics_0.36.0 workflowr_1.6.2    

loaded via a namespace (and not attached):
  [1] colorspace_1.4-1            hwriter_1.3.2              
  [3] ellipsis_0.3.1              rprojroot_1.3-2            
  [5] XVector_0.30.0              GenomicRanges_1.42.0       
  [7] ggdendro_0.1.22             fs_1.5.0                   
  [9] rstudioapi_0.11             farver_2.0.3               
 [11] ggrepel_0.8.2               DT_0.16                    
 [13] fansi_0.4.1                 lubridate_1.7.9            
 [15] xml2_1.3.2                  leaps_3.1                  
 [17] knitr_1.30                  jsonlite_1.7.1             
 [19] Rsamtools_2.6.0             Cairo_1.5-12.2             
 [21] broom_0.7.2                 cluster_2.1.0              
 [23] dbplyr_2.0.0                png_0.1-7                  
 [25] compiler_4.0.3              httr_1.4.2                 
 [27] backports_1.2.0             assertthat_0.2.1           
 [29] Matrix_1.2-18               lazyeval_0.2.2             
 [31] cli_2.1.0                   later_1.1.0.1              
 [33] htmltools_0.5.0             tools_4.0.3                
 [35] gtable_0.3.0                GenomeInfoDbData_1.2.4     
 [37] reshape2_1.4.4              FactoMineR_2.3             
 [39] ShortRead_1.48.0            Rcpp_1.0.5                 
 [41] Biobase_2.50.0              cellranger_1.1.0           
 [43] vctrs_0.3.4                 Biostrings_2.58.0          
 [45] crosstalk_1.1.0.1           xfun_0.19                  
 [47] rvest_0.3.6                 lifecycle_0.2.0            
 [49] zlibbioc_1.36.0             MASS_7.3-53                
 [51] zoo_1.8-8                   hms_0.5.3                  
 [53] promises_1.1.1              MatrixGenerics_1.2.0       
 [55] SummarizedExperiment_1.20.0 RColorBrewer_1.1-2         
 [57] latticeExtra_0.6-29         stringi_1.5.3              
 [59] highr_0.8                   S4Vectors_0.28.0           
 [61] BiocParallel_1.24.0         GenomeInfoDb_1.26.0        
 [63] rlang_0.4.8                 pkgconfig_2.0.3            
 [65] matrixStats_0.57.0          bitops_1.0-6               
 [67] evaluate_0.14               lattice_0.20-41            
 [69] labeling_0.4.2              GenomicAlignments_1.26.0   
 [71] htmlwidgets_1.5.2           tidyselect_1.1.0           
 [73] here_0.1                    plyr_1.8.6                 
 [75] magrittr_1.5                R6_2.5.0                   
 [77] IRanges_2.24.0              generics_0.1.0             
 [79] DelayedArray_0.16.0         DBI_1.1.0                  
 [81] pillar_1.4.6                haven_2.3.1                
 [83] whisker_0.4                 withr_2.3.0                
 [85] scatterplot3d_0.3-41        RCurl_1.98-1.2             
 [87] modelr_0.1.8                crayon_1.3.4               
 [89] rmarkdown_2.5               jpeg_0.1-8.1               
 [91] grid_4.0.3                  readxl_1.3.1               
 [93] data.table_1.13.2           git2r_0.27.1               
 [95] reprex_0.3.0                digest_0.6.27              
 [97] flashClust_1.01-2           httpuv_1.5.4               
 [99] stats4_4.0.3                munsell_0.5.0              
[101] viridisLite_0.3.0